1 /********************
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2 * 2004 Jalview Reengineered
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12 package jalview.gui;
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14 import jalview.jbgui.GAlignFrame;
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15 import jalview.schemes.*;
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16 import jalview.datamodel.*;
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17 import jalview.analysis.*;
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18 import jalview.io.*;
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21 import java.awt.event.*;
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22 import java.awt.print.*;
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23 import javax.swing.*;
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24 import javax.swing.event.*;
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27 public class AlignFrame extends GAlignFrame
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29 final AlignmentPanel alignPanel;
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30 final AlignViewport viewport;
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31 public AlignFrame(AlignmentI al)
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34 viewport = new AlignViewport(al,true,true,true,false);
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35 alignPanel = new AlignmentPanel(this, viewport);
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36 getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
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37 fontNameMenuItem.setText(viewport.getFont().getName());
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38 fontSizeMenuItem.setText(viewport.getFont().getSize()+"");
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41 protected void saveAs_actionPerformed(ActionEvent e)
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43 JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);
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44 chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
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45 chooser.setToolTipText("Save");
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46 int value = chooser.showSaveDialog(this);
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47 if(value == JFileChooser.APPROVE_OPTION)
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49 String choice = chooser.getSelectedFile().getPath();
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50 jalview.bin.Cache.LAST_DIRECTORY = choice;
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51 String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
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53 java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
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54 out.println(output);
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57 catch(Exception ex){}
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62 protected void outputText_actionPerformed(ActionEvent e)
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64 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
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65 JInternalFrame frame = new JInternalFrame();
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66 cap.formatForOutput();
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67 frame.setContentPane(cap);
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68 Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
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69 cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
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72 protected void htmlMenuItem_actionPerformed(ActionEvent e)
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74 HTMLOutput htmlOutput = new HTMLOutput(viewport);
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78 public void printMenuItem_actionPerformed(ActionEvent e)
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80 //Putting in a thread avoids Swing painting problems
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81 PrintThread thread = new PrintThread();
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85 class PrintThread extends Thread
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89 PrinterJob printJob = PrinterJob.getPrinterJob();
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90 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
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91 printJob.setPrintable(alignPanel, pf);
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92 if (printJob.printDialog())
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98 catch (Exception PrintException)
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100 PrintException.printStackTrace();
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110 public void closeMenuItem_actionPerformed(ActionEvent e)
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113 this.setClosed(true);
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114 }catch(Exception ex){}
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117 ArrayList historyList = new ArrayList();
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118 ArrayList redoList = new ArrayList();
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120 void updateEditMenuBar()
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122 if(historyList.size()>0)
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124 undoMenuItem.setEnabled(true);
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125 Object [] history = (Object[])historyList.get(0);
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126 undoMenuItem.setText("Undo "+history[0]);
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130 undoMenuItem.setEnabled(false);
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131 undoMenuItem.setText("Undo");
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134 if(redoList.size()>0)
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136 redoMenuItem.setEnabled(true);
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137 Object [] history = (Object[])redoList.get(0);
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138 redoMenuItem.setText("Redo "+history[0]);
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142 redoMenuItem.setEnabled(false);
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143 redoMenuItem.setText("Redo");
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147 public void addHistoryItem(String type)
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149 // must make sure we add new sequence objects her, not refs to the existing sequences
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151 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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152 for(int i=0; i<viewport.getAlignment().getHeight(); i++)
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154 seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),
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155 viewport.getAlignment().getSequenceAt(i).getSequence());
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158 historyList.add(0, new Object[]{type, seq} );
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159 updateEditMenuBar();
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162 protected void undoMenuItem_actionPerformed(ActionEvent e)
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164 Object [] history = (Object[])historyList.remove(0);
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165 // add the redo state before continuing!!
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166 SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
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167 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
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169 seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),
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170 viewport.getAlignment().getSequenceAt(i).
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175 redoList.add(0, new Object[] {history[0], seq});
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177 seq = (SequenceI[]) history[1];
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178 viewport.setAlignment( new Alignment(seq) );
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179 updateEditMenuBar();
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180 alignPanel.RefreshPanels();
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184 protected void redoMenuItem_actionPerformed(ActionEvent e)
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186 Object [] history = (Object[])redoList.remove(0);
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187 SequenceI[] seq = (SequenceI[]) history[1];
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188 viewport.setAlignment( new Alignment(seq) );
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189 updateEditMenuBar();
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190 alignPanel.RefreshPanels();
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194 public void groupsMenuItem_actionPerformed(ActionEvent e)
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196 GroupEditor geditor = new GroupEditor(viewport, alignPanel);
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197 JInternalFrame frame = new JInternalFrame();
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198 frame.setContentPane(geditor);
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199 Desktop.addInternalFrame(frame, "Group editor", 710, 410);
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200 frame.setResizable(false);
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204 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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206 Selection sel = viewport.getSelection();
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207 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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208 sel.addElement( viewport.getAlignment().getSequenceAt(i));
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209 PaintRefresher.Refresh(null);
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212 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
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214 viewport.getSelection().clear();
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215 PaintRefresher.Refresh(null);
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218 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
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220 Selection sel = viewport.getSelection();
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221 for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
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223 if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
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224 sel.removeElement(viewport.getAlignment().getSequenceAt(i));
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226 sel.addElement(viewport.getAlignment().getSequenceAt(i));
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228 PaintRefresher.Refresh(null);
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232 public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
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234 viewport.getColumnSelection().clear();
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238 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
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240 addHistoryItem("delete columns");
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241 ColumnSelection colSel = viewport.getColumnSelection();
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242 if (colSel.size() > 0)
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244 int min = colSel.getMin();
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245 viewport.getAlignment().trimLeft(min);
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246 colSel.compensateForEdit(0,min);
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247 alignPanel.RefreshPanels();
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251 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
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253 addHistoryItem("delete columns");
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254 ColumnSelection colSel = viewport.getColumnSelection();
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255 if (colSel.size() > 0)
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257 int max = colSel.getMax();
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259 viewport.getAlignment().trimRight(max);
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261 alignPanel.RefreshPanels();
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266 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
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268 addHistoryItem("delete gapped columns");
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269 viewport.getAlignment().removeGaps();
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270 alignPanel.RefreshPanels();
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273 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
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275 addHistoryItem("delete all gaps");
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278 for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
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280 current = viewport.getAlignment().getSequenceAt(i);
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281 jSize = current.getLength();
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282 for (int j=0; j < jSize; j++)
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283 if (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || current.getCharAt(j)==' ')
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285 current.deleteCharAt(j);
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291 alignPanel.RefreshPanels();
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294 public void setGapCharMenuItem_actionPerformed(ActionEvent e)
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296 char thisChar = '-';
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297 char nextChar = '.';
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298 if(viewport.getGapCharacter()=='-')
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303 setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
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304 viewport.setGapCharacter(thisChar);
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305 alignPanel.RefreshPanels();
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308 public void findMenuItem_actionPerformed(ActionEvent e)
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310 JOptionPane op = new JOptionPane();
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311 JInternalFrame frame = op.createInternalFrame(this, "Find");
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312 Finder finder = new Finder(viewport, alignPanel, frame);
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313 frame.setContentPane(finder);
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314 frame.setSize(300,110);
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315 frame.setVisible(true);
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320 public void fontNameMenuItem_actionPerformed(ActionEvent e)
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322 String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
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325 String selection = JOptionPane.showInternalInputDialog(this,
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328 JOptionPane.QUESTION_MESSAGE,
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330 ,fontNameMenuItem.getText()).toString();
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331 if(selection!=null)
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333 fontNameMenuItem.setText(selection);
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339 public void fontSizeMenuItem_actionPerformed(ActionEvent e)
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341 String selection = JOptionPane.showInternalInputDialog(this,
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342 "Select font size",
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344 JOptionPane.QUESTION_MESSAGE,
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345 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
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346 ,fontSizeMenuItem.getText()).toString();
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347 if(selection!=null)
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349 fontSizeMenuItem.setText(selection);
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354 public void fontStyleMenuItem_actionPerformed(ActionEvent e)
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356 String selection = JOptionPane.showInternalInputDialog(this,
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357 "Select font style",
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359 JOptionPane.QUESTION_MESSAGE,
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360 null, new String[]{"plain", "bold", "italic"}
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361 ,fontStyleMenuItem.getText()).toString();
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362 if(selection!=null)
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364 fontStyleMenuItem.setText(selection);
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370 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
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372 viewport.setColourText( colourTextMenuItem.isSelected() );
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373 alignPanel.RefreshPanels();
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378 int style = java.awt.Font.PLAIN;
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379 if(fontStyleMenuItem.getText().equals("bold"))
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380 style = java.awt.Font.BOLD;
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381 else if(fontStyleMenuItem.getText().equals("italic"))
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382 style = java.awt.Font.ITALIC;
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384 viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),
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386 Integer.parseInt(fontSizeMenuItem.getText())));
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387 alignPanel.RefreshPanels();
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391 protected void wrapMenuItem_actionPerformed(ActionEvent e)
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393 viewport.setWrapAlignment( wrapMenuItem.isSelected() );
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394 alignPanel.RefreshPanels();
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398 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
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400 viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
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401 alignPanel.RefreshPanels();
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404 public void viewTextMenuItem_actionPerformed(ActionEvent e)
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406 viewport.setShowText( viewTextMenuItem.isSelected() );
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407 alignPanel.RefreshPanels();
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411 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
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413 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
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414 alignPanel.RefreshPanels();
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418 public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
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420 alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
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423 public void overviewMenuItem_actionPerformed(ActionEvent e)
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426 JInternalFrame frame = new JInternalFrame();
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427 OverviewPanel overview = alignPanel.getOverviewPanel();
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429 overview = new OverviewPanel(alignPanel, viewport);
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430 frame.setContentPane(overview);
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431 Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
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432 frame.getWidth(), frame.getHeight());
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434 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
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435 { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
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437 alignPanel.setOverviewPanel(null);
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440 alignPanel.setOverviewPanel( overview );
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442 }catch(java.lang.OutOfMemoryError ex)
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444 JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"
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445 +"\nTry reducing the font size.",
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446 "Out of memory", JOptionPane.WARNING_MESSAGE);
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452 protected void noColourmenuItem_actionPerformed(ActionEvent e)
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454 viewport.setGlobalColourScheme( null );
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455 alignPanel.setColourScheme();
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459 public void clustalColour_actionPerformed(ActionEvent e)
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461 viewport.setGlobalColourScheme(new ClustalxColourScheme( ));
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462 alignPanel.setColourScheme( );
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465 public void zappoColour_actionPerformed(ActionEvent e)
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467 viewport.setGlobalColourScheme(new ZappoColourScheme() );
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468 alignPanel.setColourScheme( );
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471 public void taylorColour_actionPerformed(ActionEvent e)
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473 viewport.setGlobalColourScheme(new TaylorColourScheme() );
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474 alignPanel.setColourScheme( );
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478 public void hydrophobicityColour_actionPerformed(ActionEvent e)
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480 viewport.setGlobalColourScheme( new HydrophobicColourScheme() );
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481 alignPanel.setColourScheme( );
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484 public void helixColour_actionPerformed(ActionEvent e)
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486 viewport.setGlobalColourScheme( new HelixColourScheme() );
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487 alignPanel.setColourScheme();
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491 public void strandColour_actionPerformed(ActionEvent e)
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493 viewport.setGlobalColourScheme(new StrandColourScheme() );
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494 alignPanel.setColourScheme( );
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498 public void turnColour_actionPerformed(ActionEvent e)
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500 viewport.setGlobalColourScheme(new TurnColourScheme() );
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501 alignPanel.setColourScheme( );
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505 public void buriedColour_actionPerformed(ActionEvent e)
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507 viewport.setGlobalColourScheme( new BuriedColourScheme() );
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508 alignPanel.setColourScheme( );
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512 protected void conservationMenuItem_actionPerformed(ActionEvent e)
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514 viewport.setConservationSelected(conservationMenuItem.isSelected());
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515 alignPanel.setColourScheme();
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517 if(conservationMenuItem.isSelected())
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519 SliderPanel sp = new SliderPanel(alignPanel, 30, true, viewport.getGlobalColourScheme());
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520 JInternalFrame frame = new JInternalFrame();
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521 frame.setContentPane(sp);
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522 Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400, 90);
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523 frame.setMaximizable(false);
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528 public void abovePIDThreshold_actionPerformed(ActionEvent e)
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530 if(abovePIDThreshold.isSelected())
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532 SliderPanel sp = new SliderPanel(alignPanel, 70, false,
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533 viewport.getGlobalColourScheme());
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534 JInternalFrame frame = new JInternalFrame();
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535 frame.setContentPane(sp);
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536 Desktop.addInternalFrame(frame, "Percentage Identity Threshold", 400, 90);
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537 frame.setMaximizable(false);
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542 public void userDefinedColour_actionPerformed(ActionEvent e)
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544 JInternalFrame frame = new JInternalFrame();
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545 UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
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546 frame.setContentPane(chooser);
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547 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
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548 frame.setResizable(false);
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549 frame.setIconifiable(false);
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550 frame.setMaximizable(false);
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553 public void PIDColour_actionPerformed(ActionEvent e)
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555 viewport.setGlobalColourScheme( new PIDColourScheme() );
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556 alignPanel.setColourScheme( );
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560 public void BLOSUM62Colour_actionPerformed(ActionEvent e)
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562 viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport) );
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563 alignPanel.setColourScheme();
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568 protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
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570 ColourKey colourKey = new ColourKey( viewport.getGlobalColourScheme() );
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571 Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);
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575 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
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577 addHistoryItem("sort");
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578 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));
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579 alignPanel.RefreshPanels();
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582 public void sortIDMenuItem_actionPerformed(ActionEvent e)
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584 addHistoryItem("sort");
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585 AlignmentSorter.sortByID( viewport.getAlignment() );
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586 alignPanel.RefreshPanels();
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589 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
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591 addHistoryItem("sort");
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592 AlignmentSorter.sortByGroup(viewport.getAlignment());
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593 AlignmentSorter.sortGroups(viewport.getAlignment());
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594 alignPanel.RefreshPanels();
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597 public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
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599 addHistoryItem("sort");
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600 if(viewport.getCurrentTree()==null)
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603 AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());
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604 alignPanel.RefreshPanels();
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607 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
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612 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
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614 if(viewport.getSelection().size()<2)
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615 JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
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618 JInternalFrame frame = new JInternalFrame();
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619 frame.setContentPane(new PairwiseAlignPanel(viewport));
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620 Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
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624 public void PCAMenuItem_actionPerformed(ActionEvent e)
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626 if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
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627 || viewport.getAlignment().getHeight()<4)
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629 JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
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630 +"at least 4 input sequences.",
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631 "Sequence selection insufficient",
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632 JOptionPane.WARNING_MESSAGE);
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637 PCAPanel pcaPanel = new PCAPanel(viewport, null);
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638 JInternalFrame frame = new JInternalFrame();
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639 frame.setContentPane(pcaPanel);
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640 Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);
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641 }catch(java.lang.OutOfMemoryError ex)
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643 JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",
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644 "Out of memory", JOptionPane.WARNING_MESSAGE);
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650 public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
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652 NewTreePanel("AV", "PID", "Average distance tree using PID");
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655 public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
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657 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
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661 protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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663 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
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666 protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
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668 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
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671 void NewTreePanel(String type, String pwType, String title)
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673 JInternalFrame frame = new javax.swing.JInternalFrame();
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675 if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
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677 tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
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678 viewport.getStartRes(), viewport.getEndRes());
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682 tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
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683 type, pwType, viewport.getStartRes(),
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684 viewport.getEndRes());
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687 frame.setContentPane(tp);
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688 Desktop.addInternalFrame(frame, title, 600, 500);
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693 public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
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695 JOptionPane.showInternalMessageDialog(this, "Jalview is currently being reengineered"
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696 +"\nwithin the Barton Group, Dundee University."
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697 +"\nThis will be available as a web service 2005",
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698 "Web service", JOptionPane.INFORMATION_MESSAGE);
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701 public void pdbTest_actionPerformed(ActionEvent e)
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703 String reply = JOptionPane.showInternalInputDialog(this, "Enter pdb code", "PDB test viewer", JOptionPane.QUESTION_MESSAGE);
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705 String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";
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706 if (reply.length()>1)
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707 url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;
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711 PDBfile pdb = new PDBfile(url,
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713 Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);
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714 seq.setPDBfile(pdb);
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715 ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;
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716 ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;
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717 // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();
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719 rotCanvas rc = new rotCanvas(pdb);
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720 JInternalFrame frame = new JInternalFrame();
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721 frame.setContentPane(rc);
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722 Desktop.addInternalFrame(frame, url, 400,400);
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724 catch (Exception ex)
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726 ex.printStackTrace();
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732 public void doKeyPressed(KeyEvent evt)
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735 System.out.println(evt.getKeyChar());
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736 if(evt.isControlDown() && evt.getKeyChar()=='f')
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737 findMenuItem_actionPerformed(null);
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